Bartender: Martini 3 Bonded Terms via Quantum Mechanics-Based Molecular Dynamics.

Coarse-grained (CG) molecular dynamics (MD) simulations have grown in applicability over the years. The recently released version of the Martini CG force field (Martini 3) has been successfully applied to simulate many processes, including protein-ligand binding. However, the current ligand parametrization scheme is manual and requires an a priori reference all-atom (AA) simulation for benchmarking. For systems with suboptimal AA parameters, which are often unknown, this translates into a CG model that does not reproduce the true dynamical behavior of the underlying molecule. Here, we present Bartender, a quantum mechanics (QM)/MD-based parametrization tool written in Go. Bartender harnesses the power of QM simulations and produces reasonable bonded terms for Martini 3 CG models of small molecules in an efficient and user-friendly manner. For small, ring-like molecules, Bartender generates models whose properties are indistinguishable from the human-made models. For more complex, drug-like ligands, it is able to fit functional forms beyond simple harmonic dihedrals and thus better captures their dynamical behavior. Bartender has the power to both increase the efficiency and the accuracy of Martini 3-based high-throughput applications by producing numerically stable and physically realistic CG models.

Glyphosate mimics 17ß-estradiol effects promoting estrogen receptor alpha activity in breast cancer cells.

Glyphosate, the active ingredient in several broad-spectrum herbicide formulations, has been validated and widely used throughout the world. Recent reports have questioned its safety, showing that glyphosate may act as an endocrine disruptor by promoting estrogenic activity. However, the molecular mechanism involved in this phenomenon remains unclear. Therefore, here we aimed to elucidate the mechanism by which glyphosate induces estrogenic activity using estrogen-sensitive breast cancer cell line models. Our results show that glyphosate mimics the cell effects of 17ß-estradiol (E2), promoting estrogen receptor α (ERα) phosphorylation, its degradation, and transcriptional activity at high concentrations. The molecular mechanism seems involved in the ERα ligand-binding domain (LBD). Molecular simulations suggest a plausible interaction between glyphosate and the LBD through a coordinated complex involving divalent cations such as Zn (II). In addition, glyphosate exposure alters the level of Cyclin-dependent kinase 7 that contribute to ERα phosphorylation. Finally, glyphosate increases cell proliferation rate and levels of cell cycle regulators, accompanied by an increase in anchorage-independent growth capacity. These findings suggest that glyphosate at high concentrations, induces estrogen-like effects through an ERα ligand binding site-dependent mechanism, leading to cellular responses resulting from a complex interplay of genomic and non-genomic events.

Hybrid QM/MM Simulations Confirm Zn(II) Coordination Sphere That Includes Four Cysteines from the P2 × 4R Head Domain.

To ascertain the role of Zn(II) as an allosteric modulator on P2X4R, QM/MM molecular dynamic simulations were performed on the WT and two P2X4R mutants suggested by previous electrophysiological data to affect Zn(II) binding. The Gibbs free energy for the reduction of the putative P2X4R Zn(II) binding site by glutathione was estimated at -22 kcal/mol. Simulations of the WT P2X4R head domain revealed a flexible coordination sphere dominated by an octahedral geometry encompassing C126, N127, C132, C149, C159 and a water molecule. The C132A mutation disrupted the metal binding site, leading to a coordination sphere with a majority of water ligands, and a displacement of the metal ion towards the solvent. The C132A/C159A mutant exhibited a tendency towards WT-like stability by incorporating the R148 backbone to the coordination sphere. Thus, the computational findings agree with previous experimental data showing Zn(II) modulation for the WT and C132A/C159A variants, but not for the C132A mutant. The results provide molecular insights into the nature of the Zn(II) modulation in P2X4R, and the effect of the C132A and C132A/C159A mutations, accounting for an elusive modulation mechanism possibly occurring in other extracellular or membrane protein.

On the physical-chemical nature of solvent polarizability and dipolarity.

The positive solvatochromism of three dyes, with a spectral behavior strongly dependents on the medium dipolarity/polarizability, was studied theoretically. Both a polarizable continuum-solvent model (CSM) and explicit solvent molecules were employed to model solvent effects. The CSM approach, coupled with ten different TDDFT methods, yielded unsatisfactory results in eleven solvents. The explicit-solvation calculations, thought of much higher computational cost, yielded excellent results. As CSM schemes are known correctly model non-specific electrostatic effects, our results indicate that the traditionally considered non-specific nature of solvent dipolarity needs to be reconsidered, requiring the explicit consideration of the solute-solvent interactions for their accurate theoretical description.

An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation.

Several different mutations of the protein copper, zinc superoxide dismutase (SOD1) produce the neurodegenerative disorder amyotrophic lateral sclerosis (ALS). The molecular mechanism by which the diverse mutations converge to a similar pathology is currently unknown. The electrostatic loop (EL) of SOD1 is known to be affected in all of the studied ALS-linked mutations of SOD1. In this work, we employ a multiscale simulation approach to show that this perturbation corresponds to an increased probability of the EL detaching from its native position, exposing the metal site of the protein to water. From extensive atomistic and coarse-grained molecular dynamics (MD) simulations, we identify an allosteric pathway that explains the action of the distant G93A mutation on the EL. Finally, we employ quantum mechanics/molecular mechanics MD simulations to show that the opening of the EL decreases the Zn(II) affinity of the protein. As the loss of Zn(II) is at the center of several proposed pathogenic mechanisms in SOD1-linked ALS, the structural effect identified here not only is in agreement with the experimental data but also places the opening of the electrostatic loop as the possible main pathogenic effect for a significant number of ALS-linked SOD1 mutations.

A comparison of computational methodologies for the structural modelling of biologically relevant zinc complexes.

The impact of a variety of modern computational methods on the structure of biologically relevant zinc complexes is studied. Different density functionals and a Hartree-Fock-based method, scalar-relativistic effects, and basis set integration grid choices, among others, are assessed for set of high-resolution crystallographic structures. While a previous study recommends incorporating relativistic effects into density functional theory calculations in order to improve the accuracy of obtained geometries for small Zn(II) coordination compounds, we show that, for the set in study, relativistic effects do not affect the geometries to a significant extent. The PBEh-3c composite method emerges as good alternative for the treatment of Zn(II) complexes, while the HF-3c method can be employed when computational efficiency is important. Graphical Abstract Which methods are best suited for the computation of Zn(II) bioligand complexes?

Insights into the halochromism of a bithiophene π* probe.

The positive halochromism of the solvatochromic 4-nitro-4'-(N,N-dimethylamino)-2,2'-bithiophene in acetone and 1-butanol was investigated by molecular dynamics simulations and quantum mechanics calculations. Interactions of the dye with the solvated sodium cation were found to have only a minor effect on the observed halochromism, which was ultimately ascribed to a predominant interaction between iodide anions and the N,N-dimethylamino group of the dye.

A benchmark for the size of the QM system required for accurate hybrid QM/MM calculations on the metal site of the protein copper, zinc superoxide dismutase.

The protein superoxide dismutase 1 (SOD1) is a copper and zinc-binding protein that has been implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS). The Zn(II) binding to SOD1 is critical for the stability of the protein, and has been by itself implicated in ALS pathogenesis. Hence, the quantum mechanical (QM) study of the Zn(II)-site of SOD1 is relevant for understanding ALS. The hybrid QM-molecular mechanics (QM/MM) approach commonly employed for the QM study of proteins is highly dependent on the size of the sub-system treated quantum-mechanically. The size of the QM system also determines the computational feasibility of a given method. In the present work, we compare optimized geometries for the metal site and Zn(II) dissociation energies obtained with a QM/MM methodology employing different sizes for the QM sub-system. We find that geometries converge rapidly to RMSDs of around 0.3 Å, and fails to converge further, while a QM system of 480 atoms was required for converging the Zn(II) interaction energy of SOD1 to within 5 kcal*mol-1, and a 611-atoms QM system for a 1 kcal*mol-1 convergence with respect to our reference, 1280 QM-atoms system. Graphical Abstract The size of the QM system is critical for both the accuracy and the computational cost of a QM/MM calculation. We have identified a optimum balance for the study of the active site of the coppper, zinc superoxide dismutase.

On the Mechanism of the Reactivity of 1,3-Dialkylimidazolium Salts under Basic to Acidic Conditions: A Combined Kinetic and Computational Study.

Comprehensive spectroscopic kinetic studies illustrate an alternative mechanism for the traditional free-carbene intermediated H/D exchange reaction of 1,3-dialkylimidazolium salts under neutral (D2 O) and acidic conditions (DCl/D2 O 35 wt % solution). The deuteration of high purity [bmim]Cl in D2 O is studied at different temperatures, in absence of catalyst or impurities, to yield an activation energy. DFT transition-state modelling, of a small water cluster and [bmim] cation, also yields an activation energy which strongly supports the proposed mechanism. The presence of basic impurities are shown to significantly enhance the exchange reaction, which brings into question the need for further analysis of technical purities of ionic liquids and the implications for a wide range of chemical reactions in such media.

A computationally-derived model for the solvatochromism of p-phenolates with high predictive power.

We report that the positive, reverse or negative solvatochromism of p-phenolate-based dyes is highly correlated with the multireferential (MR) character of their ground-state wave function, with negative compounds presenting the highest degeneracy. CASSCF/NEVPT2 calculations show that the high MR character of the wave-function in negative dyes allows those systems to increase the dipole moment of the ground state by breaking the degeneracy as a response to the field of a polar solvent. The resulting stabilization of the ground-state with increasing solvent polarity leads to the observed negative solvatochromic behavior. A computational indicator based on our results has been successfully used for determining the direction of the solvatochromic shift of 24 dyes. Thus, our work sheds light on the physical-chemical basis for solvatochromism while providing experimental chemists with a practical tool for the design of novel negative, positive or reverse solvatochromic dyes.

Insights on the Reactivity of Terminal Phosphanido Metal Complexes toward Activated Alkynes from Theoretical Computations.

Herein we present a theoretical study on the reaction of [Re(PPh2) (CO)3(phen)] (phen = 1,10-phenanthroline) and [Re(PPh2) (CO)3(bipy)] (bipy = 2,2'-bipyridine) toward methyl propiolate. In agreement with experimental results for the phen ligand, the coupling of the substituted acetylenic carbon with the nonsubstituted ortho carbon of the phen ligand is the preferred route from both kinetic and thermodynamic viewpoints with a Gibbs energy barrier of 18.8 kcal/mol and an exoergicity of 11.1 kcal/mol. There are other two routes, the insertion of the acetylenic fragment into the P-Re bond and the coupling between the substituted acetylenic carbon and a carbonyl ligand in cis disposition, which are kinetically less favorable than the preferred route (by 2.8 and 1.9 kcal/mol, respectively). Compared with phen, the bipy ligand shows less electrophilic character and also less π electron delocalization due to the absence of the fused ring between the two pyridine rings. As a consequence, the route involving the coupling with a carbonyl ligand starts to be kinetically competitive, whereas the product of the attack to bipy is still the most stable and would be the one mainly obtained after spending enough time to reach thermal equilibrium.

Nuclear Magnetic Shieldings of Stacked Aromatic and Antiaromatic Molecules.

Nuclear magnetic shieldings have been calculated at the density functional theory (DFT) level for stacks of benzene, hexadehydro[12]annulene, dodecadehydro[18]annulene, and hexabenzocoronene. The magnetic shieldings due to the ring currents in the adjacent molecules have been estimated by calculating nucleus independent molecular shieldings for the monomer in the atomic positions of neighbor molecules. The calculations show that the independent shielding model works reasonably well for the 1H NMR shieldings of benzene and hexadehydro[12]annulene, whereas for the larger molecules and for the 13C NMR shieldings the interaction between the molecules leads to shielding effects that are at least of the same size as the ring current contributions from the adjacent molecules. A better agreement is obtained when the nearest neighbors are also considered at full quantum mechanical (QM) level. The calculations suggest that the nearest solvent molecules must be included in the quantum mechanical system, at least when estimating solvent shifts at the molecular mechanics (MM) level. Current density calculations show that the stacking does not significantly affect the ring current strengths of the individual molecules, whereas the shape of the ring current for a single molecule differs from that of the stacked molecules.

Calculations of the light absorption spectra of porphyrinoid chromophores for dye-sensitized solar cells.

Solar power is a strong alternative to the currently used fossil fuels in order to satisfy the world's energy needs. Among them, dye-sensitized solar cells (DSSC) represent a low-cost option. Efficient and cheap dyes are currently needed to make DSSCs competitive. Computational chemistry can be used to guide the design of new light-absorbing chromophores. Here, we have computationally studied the lowest excited states of ZnPBAT, which is a recently synthesized porphyrinoid chromophore with high light-absorption efficiency. The calculations have been performed at ab initio correlated levels of theory employing second-order coupled clusters (CC2) and algebraic diagrammatic construction using second order (ADC(2)) methods and by performing density functional theory (DFT) calculations using the time-dependent DFT (TDDFT) approach for excitation energies. The ultraviolet-visible (UV-vis) spectrum calculated at the ADC(2) and CC2 levels agrees well with the experimental one. The calculations show that ZnPBAT has six electronic transitions in the visible range of the absorption spectrum. The ab initio correlated calculations and previously reported experimental data have been used to assess the performance of several well-known density functionals that have been employed in the present TDDFT study. Solvent effects have been estimated by using the conductor-like screening model (COSMO). The influence of the addition of a TiO2 cluster to the chromophore systems has also been investigated. The results indicate that both CAM-B3LYP and Becke's "half-and-half" (BHLYP) density functionals are appropriate for the studies of excitation energies in the blue range of the visible spectrum for these kinds of porphyrinoid chromophores, whereas the excitation energies of the Q band calculated at the ab initio correlated level are more accurate than those obtained in the present TDDFT calculations. The inclusion of solvent effects has a modest influence on the spectrum of the protonated form of the studied chromophores, whereas solvent models are crucial when studying the absorption spectrum of the anionic chromophore. The calculated UV-vis spectrum for the chromophore anion is not significantly affected by attaching a TiO2 cluster to it.

Destabilization of the metal site as a hub for the pathogenic mechanism of five ALS-linked mutants of copper, zinc superoxide dismutase.

Amyotrophic lateral sclerosis (ALS) is a lethal neurodegenerative disease, with no effective pharmacological treatment. Its pathogenesis is unknown, although a subset of the cases is linked to genetic mutations. A significant fraction of the mutations occur in one protein, copper, zinc superoxide dismutase (SOD1). The toxic function of mutant SOD1 has not been elucidated, but damage to the metal site of the protein is believed to play a major role. In this work, we study the electrostatic loop of SOD1, which we had previously proposed to work as a "solvent seal" isolating the metal site from water molecules. Out of the five contact points identified between the electrostatic loop and its dock in the rest of the protein, three points were found to be affected by ALS-linked mutations, with a total of five mutations identified. The effect of the five mutations was studied using methods of computational chemistry. We found that four of the mutations destabilize the proposed solvent seal, while the fifth mutation directly affects the metal-site stability. In the two contact points unaffected by ALS-linked mutations, the side chains of the residues were not found to play a stabilizing role. Our results show that the docking of the electrostatic loop to the rest of SOD1 plays a role in ALS pathogenesis, in support of that structure acting as a solvent barrier for the metal site. The results provide a unified pathogenic mechanism for five different ALS-linked mutations of SOD1.

Effect of including torsional parameters for histidine-metal interactions in classical force fields for metalloproteins.

Classical force-field parameters of the metal site of metalloproteins usually comprise only the partial charges of the involved atoms, as well as the bond-stretching and bending parameters of the metal-ligand interactions. Although for certain metal ligands such as histidine residues, the torsional motions at the metal site play an important role for the dynamics of the protein, no such terms have been considered to be crucial in the parametrization of the force fields, and they have therefore been omitted in the parametrization. In this work, we have optimized AMBER-compatible force-field parameters for the reduced state of the metal site of copper, zinc superoxide dismutase (SOD1) and assessed the effect of including torsional parameters for the histidine-metal interactions in molecular dynamics simulations. On the basis of the obtained results, we recommend that torsion parameters of the metal site are included when processes at the metal site are investigated or when free-energy calculations are performed. As the torsion parameters mainly affect the structure of the metal site, other kinds of structural studies can be performed without considering the torsional parameters of the metal site.

Capricious selectivity in electrophilic deuteration of methylenedioxy substituted aromatic compounds.

Ring deuteration via the SEAr mechanism, which is usually problem-free, is found to be troublesome with methylenedioxy substituent aromatics. We report a case where the deuteration not only partially fails at one of the ortho positions but also is completely prevented by a conformation dependent effect at the other o-position. Such selectivity discrepancies are important due to the widespread occurrence of methylenedioxy substituted natural products. Density functional theory calculations were used to elucidate the exchange reaction mechanism in 1,2-dialkoxybenzenes.

The role of solvent exclusion in the interaction between D124 and the metal site in SOD1: implications for ALS.

Structural changes in the metal site of the copper-zinc superoxide dismutase (SOD1) are involved in the various mechanisms proposed for the pathogenesis of the SOD1-linked familial form of amyotrophic lateral sclerosis (ALS). Elucidating how the metal site of SOD1 can be disrupted by ALS-linked mutations is important for a better understanding of the pathogenesis of the disease and for developing more efficient treatments. Residue D124, a second-sphere ligand of the copper and zinc ions, is known from experimental studies to be essential for the integrity of the metal-site structure. In this work, we used density functional theory calculations and molecular dynamics simulations to elucidate which factors keep D124 attached to the metal site and how structural changes may disrupt the binding between D124 and the metal first-sphere ligands. The calculations show that D124 is kept attached to the metal site in a kinetic trap. The exclusion of solvent molecules by the electrostatic loop of the protein is found to create the binding of D124 to the metal site. The calculations also indicate that changes in the structure of the electrostatic loop of the protein can weaken the D124-metal site interaction, lowering the affinity of the zinc site for the metal. Destabilization of the electrostatic loop of SOD1 has been previously shown to be a common property of ALS-linked variants of the protein, but its role in the pathogenesis of SOD1-linked ALS has not been elucidated.

Computational studies of the metal-binding site of the wild-type and the H46R mutant of the copper, zinc superoxide dismutase.

Impairment of the Zn(II)-binding site of the copper, zinc superoxide dismutase (CuZnSOD) protein is involved in a number of hypotheses and explanations for the still unknown toxic gain of function mutant varieties of CuZnSOD that are associated with familial forms of amyotrophic lateral sclerosis (ALS). In this work, computational chemistry methods have been used for studying models of the metal-binding site of the ALS-linked H46R mutant of CuZnSOD and of the wild-type variety of the enzyme. By comparing the energy and electronic structure of these models, a plausible explanation for the effect of the H46R mutation on the zinc site is obtained. The computational study clarifies the role of the D124 and D125 residues for keeping the structural integrity of the Zn(II)-binding site, which was known to exist but its mechanism has not been explained. Earlier results suggest that the explanation for the impairment of the Zn(II)-site proposed in this work may be useful for understanding the mechanism of action of the ALS-linked mutations in CuZnSOD in general.

A computationally efficient and reliable bond order measure.

Bond order indexes are useful measures that connect quantum mechanical results with chemical understanding. One of these measures, the natural bond order index, based on the natural resonance theory procedure and part of the natural bond orbital analysis tools, has been proved to yield reliable results for many systems. The procedure's computational requirements, nevertheless, scales so highly with the number of functions in the basis set and the delocalization of the system, that the calculation of this bond order is limited to small or medium size molecules. We present in this work a bond order index, the first order perturbation theory bond order (fopBO), which is based on and strongly connected to the natural bond orbital analysis tools. We present the methodology for the calculation of the fopBO index and a number of test calculations that shows that it is as reliable as the natural bond orbital index, with the same weak sensitivity to variations among commonly used basis sets and, as opposed to the natural bond order index, suitable for the study of large systems, such as most of those of biological interest.